diff splicesite.xml @ 14:76e1b1b21cce default tip

Deleted selected files

--- a/splicesite.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-<tool id="splicesite" name="splice site score">
-  <description>using max entropy model</description>
-  <command interpreter="perl">$script $input > $out_file1 </command>
-  <inputs>
-    <param name="input" format="txt" type="data" label="Sequence file" help="fasta or raw sequence (one sequence per line)"/>
-    <param name="script" type="select" label="Select model">
-        <option value="splicesitescore/score5.pl" selected="true">5' splice site</option>
-        <option value="splicesitescore/score3.pl">3' splice site</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="tabular" name="out_file1" />
-  </outputs>
-  <help>
-
-**What it does**
-
-This tool computes splice site scores using a max entropy model. See more details here: 
-
-http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html
-
------
-
-**Example input for 5' splice site sequence**
-
-3 exonic and 6 intronic nucleotides flanking the junction::
-
-    CTGGTGAGT
-    AAGGTACAG
-
-or fasta format::
-
-    >seq1
-    CTGGTGAGT
-    >seq2
-    AAGGTACAG
-
-Output::
-
-    CTGGTGAGT	10.10
-    AAGGTACAG	8.04
-
-or fasta format::
-
-    >seq1   CTGGTGAGT	10.10
-    >seq2   AAGGTACAG	8.04
-
-
------
-
-**Example input for 3' splice site sequence**
-
-3 exonic and 20 intronic nucleotides flanking the junction::
-
-    CCTGCATCCTCTGTTCCCAGGTG
-    TTTCTTCCCTCCGGGAACAGTGG
-
-Output::
-
-    CCTGCATCCTCTGTTCCCAGGTG	10.47
-    TTTCTTCCCTCCGGGAACAGTGG	6.22
-
-  </help>
-</tool>